IMPACT_S

Class Utilities

java.lang.Object

IMPACT_S.Utilities

public class Utilities
extends java.lang.Object

Utilities used across the whole software package.

Author:

Emanuel Maldonado

See Also:

GUI

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ABOUTTXT_RESOURCE_PATH about text file path from IMPACT.resources
static java.lang.String	ATVExeKey ATV program location
static java.lang.String	BaseKey GUI Base directory location
static java.lang.String	CodemlExeKey Codeml program location
static java.lang.String	DatamonkeyDataKey GUI Datamonkey data location
static java.lang.String	DatamonkeyResDirName GUI Datamonkey tab results directory name.
static java.lang.String	DataSetDirName GUI base data sets directory name.
static java.lang.String	DataSetKey GUI DataSet directory location
static java.lang.String	GNUPLOTExeKey Gnuplot program location
static java.lang.String	IMAGE_ICON_RESOURCE_PATH image icon path from IMPACT.resources
static java.lang.String	IMAGE_INIT_RESOURCE_PATH image icon path from IMPACT.resources
static java.lang.String	JCOLOR_SCHEMES_HELP_RESOURCE_PATH image icon path from IMPACT.resources
static java.lang.String	JmolExeKey Jmol program location
static java.lang.String	lineSeparator System dependant line separator
static java.lang.String	mydfltDSName Default user defined data set name.
static java.lang.String	PAMLDataKey GUI Codeml data location
static java.lang.String	PAMLResDirName GUI Codeml tab results directory name.
static java.lang.String	PhyMLExeKey PhyML program location
static java.lang.String	PROGRAM_VERSION_RESOURCE_PATH image icon path from IMPACT.resources
static java.lang.String	programName Program name used across all modules
static java.lang.String	ProgramsKey GUI Programs directory location
static java.lang.String	Results3DDirName GUI Results tab directory name.
static java.lang.String	ResultsDataKey GUI Results & 3D data location
static java.lang.String	SystemKey GUI directory location
static java.lang.String	TreeSAAPDataKey GUI TreeSAAP data location
static java.lang.String	TreeSAAPExeKey TreeSAAP program location
static java.lang.String	TreeSAAPResDirName GUI TreeSAAP tab results directory name.

Constructor Summary

Constructors

Constructor and Description
Utilities() Empty constructor.

Method Summary

Modifier and Type	Method and Description
int	countCharAt(java.lang.String str, char chsearch) Count occurrences of char in string.
boolean	downloadFile(java.lang.String uurl, java.io.File tmpout) Download file pointed by url to file.
java.lang.String	firstCharUp(java.lang.String txt) Get given string with only first character to upper case. Remaining part to lower case.
java.lang.String[]	getArrayObjectToStr(java.lang.Object[] values) Produce an String array from an Object array.
java.io.BufferedReader	getBR(java.lang.String filepath) Get Buffered Reader for file reading.
java.lang.String	getCodemlDir() Get codeml directory.
java.lang.String	getExt(java.lang.String filename) Get filename extension.
java.lang.String	getFallBackLocation(java.lang.String key) Get location given associated key.
java.lang.String	getFileContent(java.io.InputStream file) Get content of file, by input stream.
java.lang.String	getFileContent(java.lang.String filepath) Get file content for specified file.
int	getIntegerFromStr(java.lang.String str) Given a string comprised by text and numbers, get the first number found in string.
int[]	getIntegersFrom(java.lang.String[] ints, boolean sort, boolean asc) Get array of integers from array of strings consisting of only integers.
java.lang.String	getLocation(java.lang.String key) Get location given associated key.
java.lang.String	getName(java.lang.String path) Get name of file given absolute path. For opposite see also.
java.lang.String	getNameNoExt(java.lang.String pathtofile) Remove extension from filename with extension, given absolute path to filename.
java.lang.String	getNewGenFile(java.lang.String filePath, java.lang.String fileName) For given file absolute path (with no name), calculates new name until it is found not to exist. If it is needed (&99) number of generation IDs may be extended.
java.lang.String	getPathNoName(java.lang.String path) Get path without file name, given absolute path. For opposite see also.
java.lang.String	getRGBColor(java.lang.String clrtostr, java.lang.String useparentesis) Get color given by Color.toString() in format r,g,b only.
java.lang.String	getSubstrChopFst(java.lang.String txt) Get substring without first character.
java.lang.String	getSubstrChopLast(java.lang.String txt) Get substring without last character.
java.lang.String	getSubstringByChar(java.lang.String text, java.lang.String ch) Get substring from text given char. The final string consists of all characters between 0 and index of that character.
java.lang.String	join(java.lang.String[] p, java.lang.String charsep) Build a string from an array with elements separated by charsep.
void	println(java.lang.String msg)
boolean	renameFile(java.lang.String source, java.lang.String dest, boolean deletesrc) Copies content from source file to destination file. This way creating a rename operation. This was created to overcome limitations of File.renameTo() method. Replaces any destination file that may exist.
java.lang.String	replaceExtBy(java.lang.String filename, java.lang.String newExt) Replace extension with new given extension.
void	setLocation(java.lang.String key, java.lang.String value) Set location to key.
boolean	startUtilities() Start initialization of necessary locations.
void	updateTreeSAAPBS() Update TreeSAAP baseml settings file.
void	updateTreeSAAPDS() Update TreeSAAP driver settings file to work with TreeSAAP tab output directory.
void	updateTreeSAAPDtS() Update TreeSAAP data settings file.
void	updateTreeSAAPGS() Update TreeSAAP gui settings file.
void	updateTreeSAAPSettings() Update TreeSAAP Settings files.
void	writePreferences(boolean useds) Save (user) preferences to file.
java.lang.String	writeToFile(java.lang.String[] content, java.lang.String header, java.lang.String filename) Write an array of lines to file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

lineSeparator

public static final java.lang.String lineSeparator

System dependant line separator

programName

public static final java.lang.String programName

Program name used across all modules

See Also:

Constant Field Values

mydfltDSName

public static final java.lang.String mydfltDSName

Default user defined data set name.

See Also:

Constant Field Values

BaseKey

public static final java.lang.String BaseKey

GUI Base directory location

See Also:

Constant Field Values

SystemKey

public static final java.lang.String SystemKey

GUI directory location

See Also:

Constant Field Values

ProgramsKey

public static final java.lang.String ProgramsKey

GUI Programs directory location

See Also:

Constant Field Values

DataSetKey

public static final java.lang.String DataSetKey

GUI DataSet directory location

See Also:

Constant Field Values

TreeSAAPDataKey

public static final java.lang.String TreeSAAPDataKey

GUI TreeSAAP data location

See Also:

Constant Field Values

DatamonkeyDataKey

public static final java.lang.String DatamonkeyDataKey

GUI Datamonkey data location

See Also:

Constant Field Values

PAMLDataKey

public static final java.lang.String PAMLDataKey

GUI Codeml data location

See Also:

Constant Field Values

ResultsDataKey

public static final java.lang.String ResultsDataKey

GUI Results & 3D data location

See Also:

Constant Field Values

CodemlExeKey

public static final java.lang.String CodemlExeKey

Codeml program location

See Also:

Constant Field Values

PhyMLExeKey

public static final java.lang.String PhyMLExeKey

PhyML program location

See Also:

Constant Field Values

ATVExeKey

public static final java.lang.String ATVExeKey

ATV program location

See Also:

Constant Field Values

JmolExeKey

public static final java.lang.String JmolExeKey

Jmol program location

See Also:

Constant Field Values

TreeSAAPExeKey

public static final java.lang.String TreeSAAPExeKey

TreeSAAP program location

See Also:

Constant Field Values

GNUPLOTExeKey

public static final java.lang.String GNUPLOTExeKey

Gnuplot program location

See Also:

Constant Field Values

DataSetDirName

public static final java.lang.String DataSetDirName

GUI base data sets directory name.

See Also:

Constant Field Values

TreeSAAPResDirName

public static final java.lang.String TreeSAAPResDirName

GUI TreeSAAP tab results directory name.

See Also:

Constant Field Values

DatamonkeyResDirName

public static final java.lang.String DatamonkeyResDirName

GUI Datamonkey tab results directory name.

See Also:

Constant Field Values

PAMLResDirName

public static final java.lang.String PAMLResDirName

GUI Codeml tab results directory name.

See Also:

Constant Field Values

Results3DDirName

public static final java.lang.String Results3DDirName

GUI Results tab directory name.

See Also:

Constant Field Values

IMAGE_ICON_RESOURCE_PATH

public static java.lang.String IMAGE_ICON_RESOURCE_PATH

image icon path from IMPACT.resources

IMAGE_INIT_RESOURCE_PATH

public static java.lang.String IMAGE_INIT_RESOURCE_PATH

image icon path from IMPACT.resources

JCOLOR_SCHEMES_HELP_RESOURCE_PATH

public static java.lang.String JCOLOR_SCHEMES_HELP_RESOURCE_PATH

image icon path from IMPACT.resources

ABOUTTXT_RESOURCE_PATH

public static java.lang.String ABOUTTXT_RESOURCE_PATH

about text file path from IMPACT.resources

PROGRAM_VERSION_RESOURCE_PATH

public static java.lang.String PROGRAM_VERSION_RESOURCE_PATH

image icon path from IMPACT.resources

Constructor Detail

Utilities

public Utilities()

Empty constructor.

Method Detail

println

public void println(java.lang.String msg)

startUtilities

public boolean startUtilities()

Start initialization of necessary locations.

Returns:

false if successful start; true, otherwise.

writePreferences

public void writePreferences(boolean useds)

Save (user) preferences to file.

Parameters:

useds - true, to save Dataset locations.

getLocation

public java.lang.String getLocation(java.lang.String key)

Get location given associated key.

Parameters:

key - to identify location.

Returns:

location associated to key.

getFallBackLocation

public java.lang.String getFallBackLocation(java.lang.String key)

Get location given associated key. If given key has empty value, fall back to Base path.

Parameters:

key - to identify location.

Returns:

location associated to key.

setLocation

public void setLocation(java.lang.String key,
                        java.lang.String value)

Set location to key.

Parameters:

key - to identify location to be changed.

value - of location.

getCodemlDir

public java.lang.String getCodemlDir()

Get codeml directory. This is obtained by location of codeml executable.

Returns:

codeml executable directory absolute path.

join

public java.lang.String join(java.lang.String[] p,
                             java.lang.String charsep)

Build a string from an array with elements separated by charsep.

Parameters:

p - array to join.

charsep - choose which character will separate contents of p. TAB is used if null.

Returns:

string representing array p

getSubstrChopLast

public java.lang.String getSubstrChopLast(java.lang.String txt)

Get substring without last character.

Parameters:

txt - string 'txt'

Returns:

substring 'tx'

getSubstrChopFst

public java.lang.String getSubstrChopFst(java.lang.String txt)

Get substring without first character.

Parameters:

txt - string 'txt'

Returns:

substring 'xt'

getSubstringByChar

public java.lang.String getSubstringByChar(java.lang.String text,
                                           java.lang.String ch)

Get substring from text given char.
The final string consists of all characters between 0 and index of that character.

Parameters:

text - from where to search and get final result.

ch - the character to search.

Returns:

substring from 0 to index of char (excluding char); or empty string "", if not found.

firstCharUp

public java.lang.String firstCharUp(java.lang.String txt)

Get given string with only first character to upper case.
Remaining part to lower case.

Parameters:

txt - string 'txt'

Returns:

string 'Txt'; if txt is null or empty, empty is returned.

getName

public java.lang.String getName(java.lang.String path)

Get name of file given absolute path.
For opposite see also.

Parameters:

path - file (absolute) path

Returns:

name of directory (chopped path)

See Also:

getPathNoName(String path)

getPathNoName

public java.lang.String getPathNoName(java.lang.String path)

Get path without file name, given absolute path.
For opposite see also.

Parameters:

path - absolute path to file.

Returns:

path only (chopped name)

See Also:

getName(String path)

getExt

public java.lang.String getExt(java.lang.String filename)

Get filename extension.

Parameters:

filename - with extension.

Returns:

extension without '.' ; null if filename has no extension.

replaceExtBy

public java.lang.String replaceExtBy(java.lang.String filename,
                                     java.lang.String newExt)

Replace extension with new given extension.

Parameters:

filename - with extension.

newExt - of the new extension.

Returns:

filename with new extension.

getNameNoExt

public java.lang.String getNameNoExt(java.lang.String pathtofile)

Remove extension from filename with extension, given absolute path to filename.

Parameters:

pathtofile - with extension

Returns:

filename without extension excluding the dot; or filename if no extension.

getNewGenFile

public java.lang.String getNewGenFile(java.lang.String filePath,
                                      java.lang.String fileName)

For given file absolute path (with no name), calculates new name until it is found not to exist.
If it is needed (&99) number of generation IDs may be extended.

Parameters:

filePath - path of file (only directory(ies)).

fileName - name of file with extension.

Returns:

new generated absolute file path that does not exist. With same extension.

getBR

public java.io.BufferedReader getBR(java.lang.String filepath)

Get Buffered Reader for file reading.

Parameters:

filepath - absolute path for file.

Returns:

br Buffered Reader

renameFile

public boolean renameFile(java.lang.String source,
                          java.lang.String dest,
                          boolean deletesrc)

Copies content from source file to destination file.
This way creating a rename operation.
This was created to overcome limitations of File.renameTo() method.
Replaces any destination file that may exist.

Parameters:

source - absolute path to source file from where to get contents.

dest - absolute path to destination file where to copy contents.

deletesrc - if true delete source file; otherwise maintain file.

Returns:

true if success; false, otherwise.

getFileContent

public java.lang.String getFileContent(java.io.InputStream file)

Get content of file, by input stream.

Parameters:

file - input stream.

Returns:

content.

getFileContent

public java.lang.String getFileContent(java.lang.String filepath)

Get file content for specified file. Content is line separated by newline.

Parameters:

filepath - absolute path.

Returns:

content; or null if file does not exist.

writeToFile

public java.lang.String writeToFile(java.lang.String[] content,
                                    java.lang.String header,
                                    java.lang.String filename)

Write an array of lines to file.

Parameters:

content - to be written to file without newlines.

header - some header to add to file (as in column names for CSV files). If this is null or empty string nothing is written.

filename - the name to be used for the file. This file will be located at Base directory if only file name is given.

Returns:

the absolute file path.

countCharAt

public int countCharAt(java.lang.String str,
                       char chsearch)

Count occurrences of char in string.

Parameters:

str - where to search for char.

chsearch - the char to search for.

Returns:

number of occurrences.

downloadFile

public boolean downloadFile(java.lang.String uurl,
                            java.io.File tmpout)

Download file pointed by url to file.

Parameters:

uurl - user url from where to download file.

tmpout - file where contents will be saved.

Returns:

true in case of success; false, otherwise.

getIntegerFromStr

public int getIntegerFromStr(java.lang.String str)

Given a string comprised by text and numbers, get the first number found in string. E.g: str = "category 65 and nine 9" will return 65.

Parameters:

str - string to be parsed.

Returns:

first number found in string.

getRGBColor

public java.lang.String getRGBColor(java.lang.String clrtostr,
                                    java.lang.String useparentesis)

Get color given by Color.toString() in format r,g,b only. It is possible to use/choose parenthesis. This must be given by string with both opening and closing, in order. E.g.: "()" or "[]", etc...

Parameters:

clrtostr - color as string. E.g.:java.awt.Color[r=200,g=0,b=0]

useparentesis - choose witch parenthesis to use; use nothing if null.

Returns:

rgb values possibly surrounded by parenthesis;
or null, if clrtostr does not, at least, contain the "[r=200,g=0,b=0]" portion.

getArrayObjectToStr

public java.lang.String[] getArrayObjectToStr(java.lang.Object[] values)

Produce an String array from an Object array.

Parameters:

values - object values.

Returns:

string values.

getIntegersFrom

public int[] getIntegersFrom(java.lang.String[] ints,
                             boolean sort,
                             boolean asc)

Get array of integers from array of strings consisting of only integers. Sort or not integers with ascending or descending order.

Parameters:

ints - array of integers as strings.

sort - if true sort final array.

asc - if sort is true, then sort by ascending (asc: true) or descending roder (asc:false).

Returns:

return array of integers sorted or not.

updateTreeSAAPSettings

public void updateTreeSAAPSettings()

Update TreeSAAP Settings files. driver, baseml, data and gui settings.

updateTreeSAAPDS

public void updateTreeSAAPDS()

Update TreeSAAP driver settings file to work with TreeSAAP tab output directory.

updateTreeSAAPDtS

public void updateTreeSAAPDtS()

Update TreeSAAP data settings file.

updateTreeSAAPBS

public void updateTreeSAAPBS()

Update TreeSAAP baseml settings file.

updateTreeSAAPGS

public void updateTreeSAAPGS()

Update TreeSAAP gui settings file.